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2019-08-08	Mark Abraham	Fix estimate of the size of a j list	commit \| commitdiff \| tree
2019-08-08	M. Eric Irrgang	Add gmxapi_pytest custom target to CMake `check` target.	commit \| commitdiff \| tree
2019-08-08	M. Eric Irrgang	Allow gmxapi Python package tests to be run from GROMACS...	commit \| commitdiff \| tree
2019-08-08	Christian Blau	Harmonize mrc density format extents with rest of code.	commit \| commitdiff \| tree
2019-08-08	M. Eric Irrgang	Reenable gtest_main target.	commit \| commitdiff \| tree
2019-08-08	Mark Abraham	Stop testing ICC on Windows	commit \| commitdiff \| tree
2019-08-08	Artem Zhmurov	Refactor Leap-Frog tests and connect them to CPU version	commit \| commitdiff \| tree
2019-08-07	M. Eric Irrgang	Use gmock and gtest targets from googletest-release...	commit \| commitdiff \| tree
2019-08-05	Pascal Merz	Move ownership of kinetic energy object to ISimulator	commit \| commitdiff \| tree
2019-08-05	Pascal Merz	Added Simulator comparison test	commit \| commitdiff \| tree
2019-08-05	Mark Abraham	Remove libgromacs_generated contributions from FindCUDA...	commit \| commitdiff \| tree
2019-08-01	Berk Hess	Remove a pointer in t_forcerec	commit \| commitdiff \| tree
2019-08-01	Berk Hess	Fix nbnxm GPU memory reservation issue	commit \| commitdiff \| tree
2019-08-01	Mark Abraham	Manage compiler flags and some include options per...	commit \| commitdiff \| tree
2019-08-01	Mark Abraham	Improve use of object libraries in libgromacs	commit \| commitdiff \| tree
2019-08-01	Mark Abraham	Merge "Merge release-2019 into master"	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Add grompp warning with use of GROMOS FF	commit \| commitdiff \| tree
2019-07-31	Artem Zhmurov	Introduce function that checks if the computations...	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Fixes for F buffer ops change	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Remove need for GROMOS FF in test	commit \| commitdiff \| tree
2019-07-31	Pascal Merz	Rename Simulator to LegacySimulator	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Move cycle counting into the GPU bonded module	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Report when development feature flags are used	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Move end of step GPU task launches to a function	commit \| commitdiff \| tree
2019-07-30	Paul Bauer	Add wrapper for outputadapter methods	commit \| commitdiff \| tree
2019-07-28	Berk Hess	Convert Ewald correction tables to C++	commit \| commitdiff \| tree
2019-07-26	Berk Hess	Add default initialization to interaction_const_t	commit \| commitdiff \| tree
2019-07-26	Christian Blau	Fix failing check-source target on python3.6	commit \| commitdiff \| tree
2019-07-25	Berk Hess	Split canDetectGpus()	commit \| commitdiff \| tree
2019-07-25	Szilárd Páll	Only stop the CUDA profiler if there are devices	commit \| commitdiff \| tree
2019-07-24	Paul Bauer	Fix doxygen in coordianteio files	commit \| commitdiff \| tree
2019-07-24	Paul Bauer	Add outputadapters (3/3)	commit \| commitdiff \| tree
2019-07-24	M. Eric Irrgang	Fix gmxapi notebook image and sample_restraint docker...	commit \| commitdiff \| tree
2019-07-24	M. Eric Irrgang	Improve gmxapi docker testing environment.	commit \| commitdiff \| tree
2019-07-23	M. Eric Irrgang	Don't install sample restraint package by default.	commit \| commitdiff \| tree
2019-07-23	Kevin Boyd	Modernize syntax of enable_if and traits to use _t...	commit \| commitdiff \| tree
2019-07-09	David van der Spoel	Fixed small bug in gmx anaeig	commit \| commitdiff \| tree
2019-07-09	M. Eric Irrgang	Incorporate sample_restraint repository.	commit \| commitdiff \| tree
2019-07-09	M. Eric Irrgang	Begin CMake front-end for Python packaging machinery.	commit \| commitdiff \| tree
2019-07-08	Szilárd Páll	Eliminate a use of double precision in the GPU bonded...	commit \| commitdiff \| tree
2019-07-08	Berk Hess	Store nbnxm gridSet data in GridSetData	commit \| commitdiff \| tree
2019-07-05	Mark Abraham	Modernize FindHwloc.cmake	commit \| commitdiff \| tree
2019-07-05	M. Eric Irrgang	Python bindings for mdrun.	commit \| commitdiff \| tree
2019-07-04	Mark Abraham	Further clang-tidy-7 fix	commit \| commitdiff \| tree
2019-07-03	Artem Zhmurov	Combine CUDA Leap-Frog, LINCS and SETTLE. II.	commit \| commitdiff \| tree
2019-07-03	Kevin Boyd	Updates to math/vec.h	commit \| commitdiff \| tree
2019-07-02	Mark Abraham	Clarify wording of release notes	commit \| commitdiff \| tree
2019-07-02	Berk Hess	Re-enable affinity diagonostics with MPI	commit \| commitdiff \| tree
2019-07-02	Kevin Boyd	Add function for calculating 3x3 matrix determinant	commit \| commitdiff \| tree
2019-07-02	Kevin Boyd	Remove references to ecutsGROUP	commit \| commitdiff \| tree
2019-07-01	Pascal Merz	Fix module detection for physical validation	commit \| commitdiff \| tree
2019-07-01	Szilárd Páll	Refactor tracking of GPU short-range work/skipping	commit \| commitdiff \| tree
2019-07-01	Berk Hess	Fix MPI deadlock in affinity setting	commit \| commitdiff \| tree
2019-07-01	M. Eric Irrgang	gmxapi Python package documentation infrastructure.	commit \| commitdiff \| tree
2019-06-30	Szilárd Páll	Create dedicated subcounter for nonbonded FEP	commit \| commitdiff \| tree
2019-06-30	Kevin Boyd	Remove group scheme checks from runner	commit \| commitdiff \| tree
2019-06-30	Magnus Lundborg	Cleaning up the GPU bonded kernel	commit \| commitdiff \| tree
2019-06-20	Paul Bauer	Use ISerializer for TPR file IO	commit \| commitdiff \| tree
2019-06-20	Berk Hess	Template free-energy kernel on soft-core	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Add BasicVector scaling, max, min and toIvec	commit \| commitdiff \| tree
2019-06-19	Szilárd Páll	Disable PME GPU on Apple OpenCL	commit \| commitdiff \| tree
2019-06-19	Berk Hess	Refactor PME atom handling	commit \| commitdiff \| tree
2019-06-19	Paul Bauer	Split tpr header reading reading from tpr body	commit \| commitdiff \| tree
2019-06-19	Berk Hess	Removed unused code paths in the NB FE kernel	commit \| commitdiff \| tree
2019-06-18	Paul Bauer	Fix gmx dump	commit \| commitdiff \| tree
2019-06-18	Mark Abraham	Move code handling mdrun -gpu_id to taskassignment...	commit \| commitdiff \| tree
2019-06-18	Berk Hess	Make forcerec const in dispatchNonbondedKernel()	commit \| commitdiff \| tree
2019-06-18	Christian Blau	Mrc format header to lattice coordinate transform	commit \| commitdiff \| tree
2019-06-18	Christian Blau	Density similarity measure and gradient	commit \| commitdiff \| tree
2019-06-18	M. Eric Irrgang	Reduce docker image size for gmxapi CI.	commit \| commitdiff \| tree
2019-06-18	Artem Zhmurov	Bug fix: Constraints tests are not instantiated with...	commit \| commitdiff \| tree
2019-06-12	Mark Abraham	Fix pygments detection for sphinx for docs build	commit \| commitdiff \| tree
2019-06-11	Mark Abraham	Use RAII approaches for hardware information detection	commit \| commitdiff \| tree
2019-06-11	Mark Abraham	Clean up multisim, communication, and REMD code	commit \| commitdiff \| tree
2019-06-11	Mark Abraham	Initialize all of gmx_domdec_comm_t	commit \| commitdiff \| tree
2019-06-11	Paul Bauer	Fix residue and molecule indexing in selections	commit \| commitdiff \| tree
2019-06-11	Berk Hess	Allow AWH geometry 'direction' to be periodic	commit \| commitdiff \| tree
2019-06-11	Paul Bauer	Add check for too many grid points in hbond	commit \| commitdiff \| tree
2019-06-05	Berk Hess	Fix reference SIMD memory alignment	commit \| commitdiff \| tree
2019-05-29	Berk Hess	Fix missing intermolecular interactions with DD	commit \| commitdiff \| tree
2019-05-29	Szilárd Páll	Template x buffer ops call on whether GPU is used	commit \| commitdiff \| tree
2019-05-27	Pascal Merz	Clean up renamed simulator.h file	commit \| commitdiff \| tree
2019-05-25	Pascal Merz	Remove dependence of mdoutf_write_to_trajectory_files...	commit \| commitdiff \| tree
2019-05-25	Pascal Merz	Rename Integrator class	commit \| commitdiff \| tree
2019-05-24	Artem Zhmurov	Clarify the EnergyOutput III	commit \| commitdiff \| tree
2019-05-24	Artem Zhmurov	Clarify the EnergyOutput II	commit \| commitdiff \| tree
2019-05-24	Mark Abraham	Reorder code before thread-MPI spawns threads	commit \| commitdiff \| tree
2019-05-23	Szilárd Páll	Fix mulitple link refs in dev-manual	commit \| commitdiff \| tree
2019-05-23	Mark Abraham	Teach ArrayRefWithPadding to make a const flavour	commit \| commitdiff \| tree
2019-05-23	Berk Hess	Fix SHAKE dH/dlambda contributions	commit \| commitdiff \| tree
2019-05-22	Mark Abraham	Rewrite starting behavior	commit \| commitdiff \| tree
2019-05-22	Mark Abraham	Introduce tri-state enums for restarts	commit \| commitdiff \| tree
2019-05-22	Alan Gray	Pin X buffer with DD and use proper abstraction in...	commit \| commitdiff \| tree
2019-05-22	Jinke Fan	Add support for Hygon Dhyana processor	commit \| commitdiff \| tree
2019-05-22	Mark Abraham	Move functionality to mdrunutility	commit \| commitdiff \| tree
2019-05-20	Mark Abraham	Fix equation typo	commit \| commitdiff \| tree
2019-05-16	Erik Lindahl	Added more quotes	commit \| commitdiff \| tree
2019-05-14	Mark Abraham	Update infrastructure needed for restart rewrite	commit \| commitdiff \| tree
2019-05-10	Paul Bauer	Remove more manual memory management	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	More Python testing infrastructure for gmxapi.	commit \| commitdiff \| tree
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